TY - JOUR
T1 - Metaproteomic investigation to assess gut microbiota shaping in newborn
mice: A combined taxonomic, functional and quantitative approach
AU - Levi Mortera, Stefano
AU - Soggiu, Alessio
AU - Vernocchi, Pamela
AU - Del Chierico, Federica
AU - Piras, Cristian
AU - Carsetti, Rita
AU - Marzano, Valeria
AU - Britti, Domenico
AU - Urbani, Andrea
AU - Roncada, Paola
AU - Putignani, Lorenza
PY - 2019
Y1 - 2019
N2 - Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition.
AB - Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition.
KW - Metaproteomics
KW - Mouse gut microbiota shaping
KW - Metaproteomics
KW - Mouse gut microbiota shaping
UR - http://hdl.handle.net/10807/153392
U2 - 10.1016/j.jprot.2019.103378
DO - 10.1016/j.jprot.2019.103378
M3 - Article
SN - 1874-3919
VL - 203
SP - 84
EP - 92
JO - Journal of Proteomics
JF - Journal of Proteomics
ER -